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Check existence output folder prior to running kraken2 #718

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Check existence output folder prior to running kraken2 #718

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11250f3
Check existence output folder prior to pipeline
TheOafidian May 9, 2023
d10a1a8
Merge branch 'DerrickWood:master' into master
TheOafidian Jun 5, 2024
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5 changes: 5 additions & 0 deletions scripts/kraken2
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,11 @@ if (! defined $threads) {
$threads = $ENV{"KRAKEN2_NUM_THREADS"} || 1;
}

if (defined $outfile && ! -f $outfile && ! -d dirname($outfile)) {
my $outdir = dirname($outfile);
die "$PROG: Output directory $outdir does not exist!\n";
}

if (! @ARGV) {
print STDERR "Need to specify input filenames!\n";
usage();
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